Diurnal variation in the human skin microbiome affects accuracy of forensic microbiome matching

Abstract Background The human skin microbiome has been recently investigated as a potential forensic tool, as people leave traces of their potentially unique microbiomes on objects and surfaces with which they interact. In this metagenomic study of four people in Hong Kong, their homes, and public surfaces in their neighbourhoods, we investigated the stability and identifiability of these microbiota traces on a timescale of hours to days. Results Using a Canberra distance-based method of comparing skin and surface microbiomes, we found that a person could be accurately matched to their household in 84% of tests and to their neighbourhood in 50% of tests, and that matching accuracy did not decay for household surfaces over the 10-day study period, although it did for public surfaces. The time of day at which a skin or surface sample was taken affected matching accuracy, and 160 species across all sites were found to have a significant variation in abundance between morning and evening samples. We hypothesised that daily routines drive a rhythm of daytime dispersal from the pooled public surface microbiome followed by normalisation of a person’s microbiome by contact with their household microbial reservoir, and Dynamic Bayesian Networks (DBNs) supported dispersal from public surfaces to skin as the major dispersal route among all sites studied. Conclusions These results suggest that in addition to considering the decay of microbiota traces with time, diurnal patterns in microbiome exposure that contribute to the human skin microbiome assemblage must also be considered in developing this as a potential forensic method.

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Metagenomic Study, Human Skin Microbiome Associated with Acne, Project

Encyclopedia of Metagenomics ◽

10.1007/978-1-4614-6418-1_532-4 ◽

2013 ◽

pp. 1-2

Author(s):

Huiying Li

Keyword(s):

Human Skin ◽

Skin Microbiome ◽

Metagenomic Study

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Metagenomic Study, Human Skin Microbiome Associated with Acne, Project

Encyclopedia of Metagenomics ◽

10.1007/978-1-4899-7475-4_532 ◽

2015 ◽

pp. 340-341

Author(s):

Huiying Li

Keyword(s):

Human Skin ◽

Skin Microbiome ◽

Metagenomic Study

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Metagenomic study of the human skin microbiome associated with acne

Nature Precedings ◽

10.1038/npre.2010.5305.1 ◽

2010 ◽

Cited By ~ 1

Author(s):

Huiying Li

Keyword(s):

Human Skin ◽

Skin Microbiome ◽

Metagenomic Study

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SkinBug: an artificial intelligence approach to predict human skin microbiome-mediated metabolism of biotics and xenobiotics

iScience ◽

10.1016/j.isci.2020.101925 ◽

2021 ◽

Vol 24 (1) ◽

pp. 101925

Author(s):

Shubham K. Jaiswal ◽

Shitij Manojkumar Agarwal ◽

Parikshit Thodum ◽

Vineet K. Sharma

Keyword(s):

Artificial Intelligence ◽

Human Skin ◽

Skin Microbiome ◽

Intelligence Approach ◽

Artificial Intelligence Approach

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Complete Genome Sequence of Malassezia restricta CBS 7877, an Opportunist Pathogen Involved in Dandruff and Seborrheic Dermatitis

Microbiology Resource Announcements ◽

10.1128/mra.01543-18 ◽

2019 ◽

Vol 8 (6) ◽

Cited By ~ 4

Author(s):

Stanislas C. Morand ◽

Morgane Bertignac ◽

Agnes Iltis ◽

Iris C. R. M. Kolder ◽

Walter Pirovano ◽

...

Keyword(s):

Human Skin ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Seborrheic Dermatitis ◽

Skin Microbiome ◽

Basidiomycetous Yeasts ◽

Content Type ◽

Opportunist Pathogen ◽

Malassezia Restricta

Malassezia restricta, one of the predominant basidiomycetous yeasts present on human skin, is involved in scalp disorders. Here, we report the complete genome sequence of the lipophilic Malassezia restricta CBS 7877 strain, which will facilitate the study of the mechanisms underlying its commensal and pathogenic roles within the skin microbiome.

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Secretory Proteases of the Human Skin Microbiome

Infection and Immunity ◽

10.1128/iai.00397-21 ◽

2021 ◽

Author(s):

Wisely Chua ◽

Si En Poh ◽

Hao Li

Keyword(s):

Human Skin ◽

Hydrolytic Enzymes ◽

Microbial Interactions ◽

Skin Microbiome ◽

Protein Cleavage ◽

Wide Range ◽

Range Of Functions ◽

Diverse Community ◽

Secreted Proteases ◽

Pathogenic Agents

The human skin is our outermost layer and serves as a protective barrier against external insults. Advances in next generation sequencing have enabled the discoveries of a rich and diverse community of microbes - bacteria, fungi and viruses that are residents of this surface. The genomes of these microbes also revealed the presence of many secretory enzymes. In particular, proteases which are hydrolytic enzymes capable of protein cleavage and degradation are of special interest in the skin environment which is enriched in proteins and lipids. In this minireview, we will focus on the roles of these skin-relevant microbial secreted proteases, both in terms of their widely studied roles as pathogenic agents in tissue invasion and host immune inactivation, and their recently discovered roles in inter-microbial interactions and modulation of virulence factors. From these studies, it has become apparent that while microbial proteases are capable of a wide range of functions, their expression is tightly regulated and highly responsive to the environments the microbes are in. With the introduction of new biochemical and bioinformatics tools to study protease functions, it will be important to understand the roles played by skin microbial secretory proteases in cutaneous health, especially the less studied commensal microbes with an emphasis on contextual relevance.

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ID3024 Polymeric nanoparticles display bactericidal effect and selective fermentation for the treatment of acne vulgaris

Biomedical Research and Therapy ◽

10.15419/bmrat.v4is.244 ◽

2017 ◽

Vol 4 (S) ◽

pp. 34

Author(s):

Ming-Fa Hsieh

Keyword(s):

Human Skin ◽

Ex Vivo ◽

Polymeric Nanoparticles ◽

Acne Vulgaris ◽

Short Chain Fatty Acids ◽

Bactericidal Effect ◽

Skin Microbiome ◽

Poly Ethylene Glycol ◽

Effective Doses ◽

Poly Ethylene

The use of antibiotics in the treatment of acne in specific group (pregnant women) of patients can lead to serious complications. We have previously demonstrated that the nanoparticles made of block copolymers of poly (ethylene glycol) and poly(e-caprolactone) can inhibit the growth of Propionibacterium acnes (P. acnes), a bacterium highly associated with the progress of acne vulgaris in the human skin [Polymers 2016; 8, 321]. To reduce the amount of antibiotics used in the treatment of skin acne, we have further demonstrated that a bacterium in the human skin microbiome can utilize PEG-based polymers to produce various short-chain fatty acids (SCFAs) which suppressed the growth of P. acnes. PEG-based polymers were chosen as selective fermentation initiators which specifically induced the fermentation of the skin commensal bacterium but not P. acnes. Interestingly, PEG-based polymers can efficiently suppress the growth of P. acnes. An acne ex vivo explant was established by using acne biopsies collected from patients with acne vulgaris at the early and middle stages. The levels of pro-inflammatory interleukin (IL)-8 cytokine in early- and middle-staged acnes were significantly higher than those in healthy skins. Incubation of acne ex vivo explants with sucrose remarkably reduced the level of IL-8 and the number of P. acnes. Results from mouse studies revealed that PEG-based polymer functions as antibiotic adjuvants which can considerably reduce the effective doses of clindamycin, a clinically-used acne antibiotic

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Anatomy promotes neutral coexistence of strains in the human skin microbiome

10.1101/2021.05.12.443817 ◽

2021 ◽

Author(s):

Arolyn Conwill ◽

Anne C Kuan ◽

Ravalika Damerla ◽

Alexandra J Poret ◽

Jacob S Baker ◽

...

Keyword(s):

Human Skin ◽

Abundant Species ◽

Therapeutic Interventions ◽

Skin Microbiome ◽

Population Fragmentation ◽

Single Strain ◽

Independent Source ◽

Cutibacterium Acnes ◽

Resident Populations ◽

And Migration

What enables strains of the same species to coexist in a microbiome? Here, we investigate if host anatomy can explain strain co-residence of Cutibacterium acnes, the most abundant species on human skin. We reconstruct on-person evolution and migration using 947 C. acnes colony genomes acquired from 16 subjects, including from individual skin pores, and find that pores maintain diversity by limiting competition. Although strains with substantial fitness differences coexist within centimeter-scale regions, each pore is dominated by a single strain. Moreover, colonies from a pore typically have identical genomes. An absence of adaptive signatures suggests a genotype-independent source of low within-pore diversity. We therefore propose that pore anatomy imposes random single-cell bottlenecks during migration into pores and subsequently blocks new migrants; the resulting population fragmentation reduces competition and promotes coexistence. Our findings imply that therapeutic interventions involving pore-dwelling species should focus on removing resident populations over optimizing probiotic fitness.

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